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EndGapFree alignments

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This commit is contained in:
Eric Coissac
2024-09-24 15:52:12 +02:00
parent 05bf2bfd6c
commit 2b4a633c30
4 changed files with 135 additions and 3 deletions
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10
pkg/obitools/obikmersim/obikmersim.go
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@@ -48,6 +48,11 @@ func MakeKmerAlignWorker[T obifp.FPUint[T]](
*slice = (*slice)[:0]
candidates := matches.Sequences()
ks := k.Kmersize
if k.SparseAt >= 0 {
ks--
}
n := candidates.Len()
for _, seq := range candidates {
idmatched_id := seq.Id()
@@ -74,6 +79,7 @@ func MakeKmerAlignWorker[T obifp.FPUint[T]](
lcons := cons.Len()
aliLength := lcons - _Abs(left) - _Abs(right)
identity := float64(match) / float64(aliLength)
residual := float64(match-int(ks)) / float64(aliLength-int(ks))
if aliLength == 0 {
identity = 0
}
@@ -93,7 +99,7 @@ func MakeKmerAlignWorker[T obifp.FPUint[T]](
rep.SetAttribute("obikmer_orientation", "reverse")
}
if aliLength >= int(k.KmerSize()) && identity >= minIdentity {
if aliLength >= int(k.KmerSize()) && residual >= minIdentity {
if withStats {
if left < 0 {
rep.SetAttribute("seq_a_single", -left)
@@ -110,6 +116,8 @@ func MakeKmerAlignWorker[T obifp.FPUint[T]](
rep.SetAttribute("seq_b_single", right)
}
rep.SetAttribute("obikmer_score", score)
rep.SetAttribute("obikmer_identity", identity)
rep.SetAttribute("obikmer_residual_id", residual)
scoreNorm := float64(0)
if aliLength > 0 {
scoreNorm = math.Round(float64(match)/float64(aliLength)*1000) / 1000